From b3380713393e0d42574174fd0a13b430b4526d25 Mon Sep 17 00:00:00 2001 From: wenruifan Date: Tue, 15 Jul 2025 14:59:46 +0100 Subject: [PATCH 1/5] Updat ecancer notebook. --- .../multiomics-cancer-classification/tutorial-cancer.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb index bf16e38..15c8441 100644 --- a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb +++ b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb @@ -481,7 +481,7 @@ "metadata": {}, "source": [ "## Step 5: Interpretation Study\n", - "We use `kale.interpret` to perform interpretation, where a function that systematically masks input features and observes the effect on performance—highlighting which features are most important for classification is provided. Please refer to [Interpret Study page](https://pykale.github.io/mmai-tutorials/tutorials/multiomics-cancer-classification/extend-reading/interpretation-study.html) for more details.\n", + "We use `kale.interpret` to perform interpretation, where a function that systematically masks input features and observes the effect on performance—highlighting which features are most important for classification is provided. Please refer to [Interpretation Study page](https://pykale.github.io/mmai-tutorials/tutorials/multiomics-cancer-classification/extend-reading/interpretation-study.html) for more details.\n", "\n", "Because the interpretation study needs us to mask one feature and observe the performance drop, we firstly define the trainer for the interpretation experiments.\n", "\n", From 7eacfa91eca6c729475c3ea837d203986fa0d32d Mon Sep 17 00:00:00 2001 From: wenruifan Date: Tue, 15 Jul 2025 15:20:34 +0100 Subject: [PATCH 2/5] Updat ecancer notebook. --- .../multiomics-cancer-classification/tutorial-cancer.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb index 15c8441..e126235 100644 --- a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb +++ b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb @@ -15,7 +15,7 @@ "id": "e0825580", "metadata": {}, "source": [ - "In this tutorial, we will use a [**M**ulti-**O**mics **G**raph c**O**nvolutional **NET**works (MOGONET) by **Wang et al. (Nature Communication, 2021)**](https://www.nature.com/articles/s41467-021-23774-w) [1] pipeline implemented in `PyKale` [2] to integrate **patient multiomics data** for **cancer classification**.\n", + "In this tutorial, we will use a [**M**ulti-**O**mics **G**raph c**O**nvolutional **NET**works (MOGONET) by **Wang et al. (Nature Communication, 2021)**](https://www.nature.com/articles/s41467-021-23774-w) [1] pipeline implemented in [`PyKale`](https://github.com/pykale/pykale#) [2] to integrate **patient multiomics data** for **cancer classification**.\n", "\n", "We will work with multiomics data from [**BRCA** of TCGA](https://www.cancerimagingarchive.net/collection/tcga-brca/) [3], which has five subtypes as the labels of classification. Three omics modalities will be used: mRNA expression, DNA methylation, and miRNA expression.\n", "\n", From 21b5daeaacaad8fd20af1d2e94f260ea46646848 Mon Sep 17 00:00:00 2001 From: wenruifan Date: Tue, 15 Jul 2025 15:21:36 +0100 Subject: [PATCH 3/5] Updat ecancer notebook. --- .../multiomics-cancer-classification/tutorial-cancer.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb index e126235..a6f8b15 100644 --- a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb +++ b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb @@ -311,7 +311,7 @@ "id": "007e4533", "metadata": {}, "source": [ - "If users are interested in more details regarding the model, please refer to the [Helper Function & Model Definition](https://pykale.github.io/mmai-tutorials/tutorials/multiomics-cancer-classification/extend-reading/helper-functions.html) of the tutorial.\n", + "If users are interested in more details regarding the model, please refer to the [Helper Function and Model Definition](https://pykale.github.io/mmai-tutorials/tutorials/multiomics-cancer-classification/extend-reading/helper-functions.html) of the tutorial.\n", "\n", "To initialize the model, we firstly call `MogonetModel` from [`model.py`](https://github.com/pykale/mmai-tutorials/blob/main/tutorials/multiomics-cancer-classification/model.py)." ] From 15248ebb4acddaae112b8762ed1a928ae7cd2411 Mon Sep 17 00:00:00 2001 From: wenruifan Date: Tue, 15 Jul 2025 15:28:24 +0100 Subject: [PATCH 4/5] Updat ecancer notebook. --- .../multiomics-cancer-classification/tutorial-cancer.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb index a6f8b15..430f785 100644 --- a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb +++ b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb @@ -93,8 +93,8 @@ " \"pykale[example]@git+https://github.com/pykale/pykale@main\" \\\n", " gdown==5.2.0 torch-geometric==2.6.0 torch_sparse torch_scatter \\\n", " -f https://data.pyg.org/whl/torch-2.6.0+cu124.html \\\n", - " && echo \"pykale, gdown, nilearn, and yacs installed successfully ✅\" \\\n", - " || echo \"Failed to install pykale, gdown, nilearn, and yacs ❌\"" + " && echo \"pykale and its requirements installed successfully ✅\" \\\n", + " || echo \"Failed to install pykale and its requirements ❌\"" ] }, { From bd615d04fe2672c5672e1a20701d2f49a8e2f3da Mon Sep 17 00:00:00 2001 From: wenruifan Date: Tue, 15 Jul 2025 15:34:28 +0100 Subject: [PATCH 5/5] Updat ecancer notebook. --- .../multiomics-cancer-classification/tutorial-cancer.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb index 430f785..dae0b2f 100644 --- a/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb +++ b/tutorials/multiomics-cancer-classification/tutorial-cancer.ipynb @@ -15,7 +15,7 @@ "id": "e0825580", "metadata": {}, "source": [ - "In this tutorial, we will use a [**M**ulti-**O**mics **G**raph c**O**nvolutional **NET**works (MOGONET) by **Wang et al. (Nature Communication, 2021)**](https://www.nature.com/articles/s41467-021-23774-w) [1] pipeline implemented in [`PyKale`](https://github.com/pykale/pykale#) [2] to integrate **patient multiomics data** for **cancer classification**.\n", + "In this tutorial, we will use a [**M**ulti-**O**mics **G**raph c**O**nvolutional **NET**works (MOGONET) by **Wang et al. (Nature Communication, 2021)**](https://www.nature.com/articles/s41467-021-23774-w) [1] pipeline implemented in [`PyKale`](https://github.com/pykale/pykale) [2] to integrate **patient multiomics data** for **cancer classification**.\n", "\n", "We will work with multiomics data from [**BRCA** of TCGA](https://www.cancerimagingarchive.net/collection/tcga-brca/) [3], which has five subtypes as the labels of classification. Three omics modalities will be used: mRNA expression, DNA methylation, and miRNA expression.\n", "\n",